Journal of Microbiology

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Paramicrobacterium salitolerans sp. nov. isolated from the agricultural soil and Microbacterium fluminis sp. nov. isolated from the Han River, South Korea: Gracia Pradnya Lolita, Do-Hoon Lee, Yong-Seok Kim, Chang-Jun Cha; Received December 19, 2025 Accepted January 20, 2026 Published online March 5, 2026; DOI: https://doi.org/10.71150/jm.2512014 [Epub ahead of print]

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Abstract PDF Supplementary Material: Two novel bacterial species, designated as CJ85^T and CJ88^T, were isolated from the agricultural soil and the Han River, South Korea, respectively. Cells of both strains were Gram-staining-positive, short rod-shaped, non-motile, and yellow-pigmented. Strain CJ85^T exhibited optimal growth in tryptic soy broth at 37°C and pH 7.0 in the absence of NaCl. Strain CJ88^T showed optimal growth in lysogeny broth at 30°C and pH 7.0 in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CJ85^T belonged to the genus Paramicrobacterium, showing the highest sequence similarity to Paramicrobacterium fandaimingii HY82^T (97.6%). Strain CJ88^T was assigned to the genus Microbacterium, with the highest sequence similarity to Microbacterium azadirachtae DSM 23848^T (98.5%). The DNA G + C content was 64.8% for strain CJ85^T and 70.5% for strain CJ88^T. The genome-based analyses, including phylogenomic tree, digital DNA-DNA hybridization, and average nucleotide identity, clearly indicated that these strains represent novel species within their respective genera. The major fatty acids of both strains were anteiso-C_15:0, anteiso-C_17:0, and iso-C_16:0. Based on the polyphasic taxonomy study, strains CJ85^T and CJ88^T represent novel species of the genera Paramicrobacterium and Microbacterium, respectively, for which names Paramicrobacterium salitolerans sp. nov. and Microbacterium fluminis sp. nov. are proposed. The type strains CJ85^T (= KACC 23064^T = JCM 36217^T) and CJ88^T (= KACC 24080^T = JCM 38050^T).

Genome-based classification of Paraniabella aurantiaca gen. nov., sp. nov., isolated from soil and taxonomic reclassification of five species within the genus Niabella: Yong-Seok Kim, Yerang Yang, Miryung Kim, Do-Hoon Lee, Chang-Jun Cha; J. Microbiol. 2025;63(10):e2505005. Published online October 31, 2025; DOI: https://doi.org/10.71150/jm.2505005

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Abstract PDF Supplementary Material: A Gram-stain-negative, aerobic, non-motile, rod-shaped, and orange-pigmented bacterium, designated CJ426^T, was isolated from ginseng soil in Anseong, Korea. Strain CJ426^T grew optimally on Reasoner’s 2A agar at 30°C and pH 7.0 in the absence of NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CJ426^T belonged to the family Chitinophagaceae and had the highest sequence similarity with Niabella hibiscisoli KACC 18857^T (98.7%). The 16S rRNA gene sequence similarities with other members of the genus Niabella ranged from 92.3% to 98.1%. Phylogenomic analyses and overall genomic relatedness indices, including average nucleotide identity, average amino acid identity, and the percentage of conserved proteins values, supported the classification of strain CJ426^T as a representative of a novel genus within the family Chitinophagaceae. Furthermore, genome-based analyses suggested that five members of the genus Niabella, including N. aquatica, N. defluvii, N. ginsengisoli, N. hibiscisoli, and, N. yanshanensis, should be separated from other Niabella species and be assigned as a novel genus. The major isoprenoid quinone of strain CJ426^T was menaquinone-7 (MK-7). The predominant polar lipids were phosphatidylethanolamine and six unidentified aminolipids. The major fatty acids were iso-C_15:0, iso-C_15:1 G, and iso-C_17:0 3-OH. The genome of strain CJ426^T was 6.3 Mbp in size, consisting of three contigs, with a G + C content of 41.9%. Based on a polyphasic taxonomic approach, strain CJ426^T represents a novel genus and species within the family Chitinophagaceae, for which the name Paraniabella aurantiaca gen. nov., sp. nov. is proposed. The type strain is CJ426^T (= KACC 23908^T = JCM 37728^T).

Comparative genomic analysis of pyrene-degrading Mycobacterium species: Genomic islands and ring-hydroxylating dioxygenases involved in pyrene degradation: Dae-Wi Kim , Kihyun Lee , Do-Hoon Lee , Chang-Jun Cha; J. Microbiol. 2018;56(11):798-804. Published online October 24, 2018; DOI: https://doi.org/10.1007/s12275-018-8372-0

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The genome sequences of two pyrene-degrading bacterial strains of Mycobacterium spp. PYR10 and PYR15, isolated from the estuarine wetland of the Han river, South Korea, were determined using the PacBio RS II sequencing platform. The complete genome of strain PYR15 was 6,037,017 bp in length with a GC content of 66.5%, and contained 5,933 protein- coding genes. The genome of strain PYR10 was 5,999,427 bp in length with a GC content of 67.7%, and contained 5,767 protein-coding genes. Based on the average nucleotide identity values, these strains were designated as M. gilvum PYR10 and M. pallens PYR15. A genomic comparison of these pyrene-degrading Mycobacterium strains with pyrene- non-degrading strains revealed that the genomes of pyrene-degrading strains possessed similar repertoires of ringhydroxylating dioxygenases (RHDs), including the pyrenehydroxylating dioxygenases encoded by nidA and nidA3, which could be readily distinguished from those of pyrenenon- degraders. Furthermore, genomic islands, containing catabolic gene clusters, were shared only among the pyrenedegrading Mycobacterium strains and these gene clusters contained RHD genes, including nidAB and nidA3B3. Our genome data should facilitate further studies on the evolution of the polycyclic aromatic hydrocarbon-degradation pathways in the genus Mycobacterium.

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